Electronic properties and absorption spectra are the grounds to investigate molecular electronic states and their interactions with the environment. Modeling and computations are required for the ...molecular understanding and design strategies of photo-active materials and sensors. However, the interpretation of such properties demands expensive computations and dealing with the interplay of electronic excited states with the conformational freedom of the chromophores in complex matrices (i.e., solvents, biomolecules, crystals) at finite temperature. Computational protocols combining time dependent density functional theory and ab initio molecular dynamics (MD) have become very powerful in this field, although they require still a large number of computations for a detailed reproduction of electronic properties, such as band shapes. Besides the ongoing research in more traditional computational chemistry fields, data analysis and machine learning methods have been increasingly employed as complementary approaches for efficient data exploration, prediction and model development, starting from the data resulting from MD simulations and electronic structure calculations. In this work, dataset reduction capabilities by unsupervised clustering techniques applied to MD trajectories are proposed and tested for the ab initio modeling of electronic absorption spectra of two challenging case studies: a non-covalent charge-transfer dimer and a ruthenium complex in solution at room temperature. The K-medoids clustering technique is applied and is proven to be able to reduce by ∼100 times the total cost of excited state calculations on an MD sampling with no loss in the accuracy and it also provides an easier understanding of the representative structures (medoids) to be analyzed on the molecular scale.
Electrons and protons are the main actors in play in proton coupled electron transfer (PCET) reactions, which are fundamental in many biological (i.e., photosynthesis and enzymatic reactions) and ...electrochemical processes. The mechanism, energetics and kinetics of PCET reactions are strongly controlled by the coupling between the transferred electrons and protons. Concerted PCET reactions are classified according to the electronical adiabaticity degree of the process. To discriminate among different mechanisms, we propose a new analysis based on the use of electron density based indexes. We choose, as test case, the 3‐Methylphenoxyl/phenol system in two different conformations to show how the proposed analysis is a suitable tool to discriminate between the different degree of adiabaticity of PCET processes. The very low computational cost of this procedure is extremely promising to analyze and provide evidences of PCET mechanisms ruling the reactivity of many biological and catalytic systems.
Concerted Proton Coupled Electron Transfer (PCET) reactions are classified according to the electronical adiabaticity degree of the process. We propose a new analysis based on the use of electron density based indexes to discriminate between different PCET mechanisms. Our analysis opens a new scenario for ab‐initio simulations to investigate complex PCET mechanisms at very low computational cost.
The Green Fluorescent Protein (GFP) is a widely studied chemical system both for its large amount of applications and the complexity of the excited state proton transfer responsible of the change in ...the protonation state of the chromophore. A detailed investigation on the structure of the chromophore environment and the influence of chromophore form (either neutral or anionic) on it is of crucial importance to understand how these factors could potentially influence the protein function. In this study, we perform a detailed computational investigation based on the analysis of
ab-initio
molecular dynamics simulations, to disentangle the main structural quantities determining the fine balance in the chromophore environment. We found that specific hydrogen bonds interactions directly involving the chromophore (or not), are correlated to quantities, such as the volume of the cavity in which the chromophore is embedded and that it is importantly affected by the chromophore protonation state. The cross-correlation analysis performed on some of these hydrogen bonds and the cavity volume, demonstrates a direct correlation among them and we also identified the ones specifically involved in this correlation. We also found that specific interactions among residues far in the space are correlated, demonstrating the complexity of the chromophore environment and that many structural quantities have to be taken into account to properly describe and understand the main factors tuning the active site of the protein. From an overall evaluation of the results obtained in this work, it is shown that the residues which
a priori
are perceived to be spectators play instead an important role in both influencing the chromophore environment (cavity volume) and its dynamics (cross-correlations among spatially distant residues).
In the search for new therapeutic strategies to contrast SARS-CoV-2, we here studied the interaction of polydatin (PD) and resveratrol (RESV)—two natural stilbene polyphenols with manifold, well ...known biological activities—with Spike, the viral protein essential for virus entry into host cells, and ACE2, the angiotensin-converting enzyme present on the surface of multiple cell types (including respiratory epithelial cells) which is the main host receptor for Spike binding. Molecular Docking simulations evidenced that both compounds can bind Spike, ACE2 and the ACE2:Spike complex with good affinity, although the interaction of PD appears stronger than that of RESV on all the investigated targets. Preliminary biochemical assays revealed a significant inhibitory activity of the ACE2:Spike recognition with a dose-response effect only in the case of PD.
Simulating the post-traumatic continuity defect of small human peripheral nerves, we compared the effectiveness of fibrin glue with neurorrhaphy for nerve gap restoration.
In twenty-four male Wistar ...rats, a fifteen mm defect in one sciatic nerve only was made and immediately repaired with an inverted polarity autograft. According to the used technique, rats were divided into Group A (Control), using traditional neurorrhaphy, and Group B (Study), using fibrine glue sealing; in total, 50% of rats were sacrificed at 16 weeks and 50% at 21 weeks. Before sacrifice, an assessment of motor function was done through Walking Track Analysis and an electroneurophysiological evaluation. After sacrifice, selected muscle mass indexes and the histology of the regenerated nerves were assessed. All data were evaluated by Student's
test for unpaired data.
No significant differences were found between the two groups, with only the exception of a relative improvement in the tibialis anterior muscle's number of motor units in the study group.
Despite the fact that the use of fibrin glue as a nerve sealant is not superior in terms of functional recovery, its effectiveness is comparable to that of microsurgical repair. Hence, the faster and technically easier glueing technique could deserve broader clinical application.
Modern, nonlinear, time-resolved spectroscopic techniques have opened new doors for investigating the intriguing but complex world of photoinduced ultrafast out-of-equilibrium phenomena and charge ...dynamics. The interaction between light and matter introduces an additional dimension, where the complex interplay between electronic and vibrational dynamics needs the most advanced theoretical–computational protocols to be fully understood on the molecular scale. In this study, we showcase the capabilities of ab initio molecular dynamics simulation integrated with a multiresolution wavelet protocol to carefully investigate the excited-state relaxation dynamics in a noncovalent complex involving tetramethylbenzene (TMB) and tetracyanoquinodimethane (TCNQ) undergoing charge transfer (CT) upon photoexcitation. Our protocol provides an accurate description that facilitates a direct comparison between transient vibrational analysis and time-resolved spectroscopic signals. This molecular level perspective enhances our understanding of photorelaxation processes confined in the adiabatic regime and offers an improved interpretation of vibrational spectra. Furthermore, it enables the quantification of anharmonic vibrational couplings between high- and low-frequency modes, specifically the TCNQ “rocking” and “bending” modes. Additionally, it identifies the primary vibrational mode that governs the adiabaticity between the ground state and the CT state. This comprehensive understanding of photorelaxation processes holds significant importance in the rational design and precise control of more efficient photovoltaic and sensor devices.
Photo‐induced charge transfer (CT) states are pivotal in many technological and biological processes. A deeper knowledge of such states is mandatory for modeling the charge migration dynamics. ...Real‐time time‐dependent density functional theory (RT‐TD‐DFT) electronic dynamics simulations are employed to explicitly observe the electronic density time‐evolution upon photo‐excitation. Asymmetrically substituted indenotetracene molecules, given their potential application as n‐type semiconductors in organic photovoltaic materials, are here investigated. Effects of substituents with different electron‐donating characters are analyzed in terms of the overall electronic energy spacing and resulting ultrafast CT dynamics through linear response (LR‐)TD‐DFT and RT‐TD‐DFT based approaches. The combination of the computational techniques here employed provided direct access to the electronic density reorganization in time and to its spatial and rational representation in terms of molecular orbital occupation time evolution. Such results can be exploited to design peculiar directional charge dynamics, crucial when photoactive materials are used for light‐harvesting applications.
The electronic layout and Real Time‐TD‐DFT electron dynamics are investigated to unveil the charge migration time evolution in two asymmetrically substituted indenotetracene compounds for potential singlet fission‐based applications in photoactive materials.
We report an extensive theoretical investigation of the photophysical properties of new carbazole core-substituted naphthalene-diimide dyes to elucidate the effects of different donor–acceptor ...arrangements on the direct and reverse intersystem crossing rates. These dyes were recently experimentally characterized using steady-state and time-resolved spectroscopy ( J. Phys. Chem. B 2021, 125, 10813 ). We analyzed the molecular structures of ground states, singlet and triplet excited states, excitation energies, orbital characteristics, and spin–orbit couplings using density functional theory (DFT)/time-dependent DFT calculations to determine the rates of the electronic spin-flip processes. Our findings reveal how different donor–acceptor configurations, by modulating ground and excited state conformational dynamics, may significantly influence the energetic landscape of singlet and triplet electronic states, their nature, and thus the extent of spin–orbit couplings, finally impacting the intersystem crossing rate constants and the reverse ones for thermally activated delayed fluorescence applications.
The interplay between light absorption and the molecular environment has a central role in the observed photophysics of a wide range of photoinduced chemical and biological phenomena. The ...understanding of the interplay between vibrational and electronic transitions is the focus of this work, since it can provide a rationale to tune the optical properties of charge transfer (CT) materials used for technological applications. A clear description of these processes poses a nontrivial challenge from both the theoretical and experimental points of view, where the main issue is how to accurately describe and probe drastic changes in the electronic structure and the ultrafast molecular relaxation and dynamics. In this work we focused on the intermolecular CT reaction that occurs upon photon absorption in a π-stacked model system in dichloromethane solution, in which the 1-chloronaphthalene (1ClN) acts as the electron donor and tetracyanoethylene (TCNE) is the electron acceptor. Density functional theory calculations have been carried out to characterize both the ground-state properties and more importantly the low-lying CT electronic transition, and excellent agreement with recently available experimental results Mathies, R. A. ; et al. J. Phys. Chem. A 2018, 122 (14), 3594 was obtained. The minima of the ground state and first singlet excited state have been accurately characterized in terms of spatial arrangements and vibrational Raman frequencies, and the CT natures of the first two low-lying electronic transitions in the absorption spectra have been addressed and clarified too. Finally, by modeling the possible coordination sites of the TCNE electron acceptor with respect to monovalent ions (Na+, K+) in an implicit solution of acetonitrile, we find that TCNE can accommodate a counterion in two different arrangements, parallel and orthogonal to the CC axis, leading to the formation of a contact ion pair. The nature of the counterion and its relative position entail structural modifications of the TCNE radical anion, mainly the central CC and CN bonds, compared to the isolated case. An important red shift of the CC stretching frequency was observed when the counterion is orthogonal to the double bond, to a greater extent for Na+. On the contrary, in the second case, where the counterion ion lies along the internuclear CC axis, we find that K+ polarizes the electron density of the double bond more, resulting in a greater red shift than with Na+.
We present electronic structure methods to unveil the non-radiative pathways of photoinduced charge transfer (CT) reactions that play a main role in photophysics and light harvesting technologies. A ...prototypical π-stacked molecular complex consisting of an electron donor (1-chloronaphthalene, 1ClN) and an electron acceptor (tetracyanoethylene, TCNE) was investigated in dichloromethane solution for this purpose. The characterization of TCNE:π:1ClN in both its equilibrium ground and photoinduced low-lying CT electronic states was performed by using a reliable and accurate theoretical-computational methodology exploiting
ab initio
molecular dynamics simulations. The structural and vibrational time evolution of key vibrational modes is found to be in excellent agreement with femtosecond stimulated Raman spectroscopy experiments R. A. Mathies
et al.
,
J. Phys. Chem. A
, 2018,
122
, 14, 3594, unveiling a correlation between vibrational fingerprints and electronic properties. The evaluation of nonadiabatic coupling matrix elements along generalized normal modes has made possible the interpretation on the molecular scale of the activation of nonradiative relaxation pathways towards the ground electronic state. In particular, two low frequency vibrational modes such as the out of plane bending and dimer breathing and the TCNE central C&z.dbd;C stretching play a prominent role in relaxation phenomena from the electronic CT state to the ground state one.
We present electronic structure methods to unveil the non-radiative pathways of photoinduced charge transfer (CT) reactions that play a main role in photophysics and light harvesting technologies.
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